Blockade of PI3Kgamma suppresses joint inflammation and damage in mouse models of rheumatoid arthritis

Phosphoinositide 3-kinases (PI3K) have long been considered promising drug targets for the treatment of inflammatory and autoimmune disorders as well as cancer and cardiovascular diseases. But the lack of specificity, isoform selectivity and poor biopharmaceutical profile of PI3K inhibitors have so far hampered rigorous disease-relevant target validation. Here we describe the identification and development of specific, selective and orally active small-molecule inhibitors of PI3Kgamma (encoded by Pik3cg). We show that Pik3cg(-/-) mice are largely protected in mouse models of rheumatoid arthritis; this protection correlates with defective neutrophil migration, further validating PI3Kgamma as a therapeutic target. We also describe that oral treatment with a PI3Kgamma inhibitor suppresses the progression of joint inflammation and damage in two distinct mouse models of rheumatoid arthritis, reproducing the protective effects shown by Pik3cg(-/-) mice. Our results identify selective PI3Kgamma inhibitors as potential therapeutic molecules for the treatment of chronic inflammatory disorders such as rheumatoid arthritis.     

Oxygen and carbon dioxide fluctuations in burrows of subterranean blind mole rats indicate tolerance to hypoxic-hypercapnic stresses

The composition of oxygen (O2), carbon dioxide (CO2), and soil humidity in the underground burrows from three species of the Israeli subterranean mole rat Spalax ehrenbergi superspecies were studied in their natural habitat. Two geographically close populations of each species from contrasting soil types were probed. Maximal CO2 levels (6.1%) and minimal O2 levels (7.2%) were recorded in northern Israel in the breeding mounds of S. carmeli in a flooded, poor drained field of heavy clay soil with very high volumetric water content. The patterns of gas fluctuations during the measurement period among the different Spalax species studied were similar. The more significant differentiation in gas levels was not among species, but between neighboring populations inhabiting heavy soils or light soils: O2 was lower and CO2 was higher in the heavy soils (clay and basaltic) compared to the relatively light soils (terra rossa and rendzina). The extreme values of gas concentration, which occurred during the rainy season, seemed to fluctuate with partial flooding of the tunnels, animal digging activity, and over-crowded breeding mounds inhabited by a nursing female and her offspring. The gas composition and soil water content in neighboring sites with different soil types indicated large differences in the levels of hypoxic-hypercapnic stress in different populations of the same species. A growing number of genes associated with hypoxic stress have been shown to exhibit structural and functional differences between the subterranean Spalax and the above-ground rat (Rattus norvegicus), probably reflecting the molecular adaptations that Spalax went through during 40 million years of evolution to survive efficiently in the severe fluctuations in gas composition in the underground habitat.     

RNA-directed construction of structurally complex and active ligase ribozymes through recombination

RNA-directed recombination can be used to catalyze a disproportionation reaction among small RNA substrates to create new combinations of sequences. But the accommodation of secondary and tertiary structural constraints in the substrates by recombinase ribozymes has not been explored. Here, we show that the Azoarcus group I intron can recombine oligoribonucleotides to construct class I ligase ribozymes, which are catalytically active upon synthesis. The substrate oligonucleotides, ranging in size from 58 to 104 nucleotides (nt), along with the 152-nt ligase ribozymes they reconstitute, can contain significant amounts of secondary structure. However, substrate recognition by the Azoarcus ribozyme depends on the existence of a single accessible CAU triplet for effective recombination. A biphasic temperature reaction profile was designed such that the sequential recombination/ligation events could take place in a thermocycler without human intervention. A temperature-dependent pH shift of the reaction buffer contributes to the success of the net reaction. When the substrate for the ligase ribozyme is introduced into the reaction mixture, as much as 11% can be observed being converted to product by the recombined ligase in the same reaction vessel. Recombination followed by ligation can also occur under isothermal conditions at 37 degrees C. Tertiary structure formation of the ligase upon construction can provide some protection from cleavage by the Azoarcus ribozyme when compared to the constituent substrates. These data suggest that RNA-directed recombination can, in fact, articulate complex ribozymes, and that there are logical rules that can guide the optimal placement of the CAU recognition sequence.     

Transcription factor binding site identification using the self-organizing map

MOTIVATION: The automatic identification of over-represented motifs present in a collection of sequences continues to be a challenging problem in computational biology. In this paper, we propose a self-organizing map of position weight matrices as an alternative method for motif discovery. The advantage of this approach is that it can be used to simultaneously characterize every feature present in the dataset, thus lessening the chance that weaker signals will be missed. Features identified are ranked in terms of over-representation relative to a background model. RESULTS: We present an implementation of this approach, named SOMBRERO (self-organizing map for biological regulatory element recognition and ordering), which is capable of discovering multiple distinct motifs present in a single dataset. Demonstrated here are the advantages of our approach on various datasets and SOMBRERO's improved performance over two popular motif-finding programs, MEME and AlignACE. AVAILABILITY: SOMBRERO is available free of charge from http://bioinf.nuigalway.ie/sombrero SUPPLEMENTARY INFORMATION: http://bioinf.nuigalway.ie/sombrero/additional.     

Chemical library synthesis using convergent approaches

New strategies are continuously being developed in combinatorial and diversity-oriented synthesis. Convergent design in target-oriented synthesis is commonly employed for construction of complex molecules. In this mini-review, we describe examples of convergent library design and synthesis as well as potential areas for future development.     

A promising biotechnical approach to pest management of Diabrotica virgifera virgifera in Illinois maize fields under kairomonal shielding with the new MSD technique

Environmentally compatible and sustainable plant protection requires novel approaches to pest management characterized by minimal emphasis on toxicants. Classical toxicants traditionally dominated economic entomology for half a century. But worldwide problems with environmental pollution and with increasing resistance levels in all major pesticide classes and in many key insect species including Diabrotica virgifera virgifera (D.v.v.) strongly advocate a rethinking and a change in management paradigms used. Soft, minimally invasive, biological, biotechnical and cultural approaches should replace hard pesticides which are in favor up to now. Fortunately, pheromones, kairomones, plant attractants, better traps, new plant varieties and cultural methods like crop rotation, in short more sophisticated methods are now available as pressure for finding and exploring novel strategies increases. Facing this situation, a new biotechnical approach of population reduction of D.v.v., called "MSD" technique, is introduced. MSD is characterized as an approach combining mass trapping, shielding and deflecting of adult insects along an invisible odor barrier of synthetic kairomone which diminishes the flux of insects across a high capacity trap line baited with kairomone, thus reducing both the population fluctuation and number and its reproductive success within the shielded area. In the case of D.v.v. in Zea mays fields, effects realized by the MSD technique have been measured simultaneously by a number of independent criteria during the summers of 2003 and 2004 at 2 different locations in Illinois maize fields of up to one half hectare size. Results observed are statistically significant and cannot be explained by mass trapping alone. There is also an additional shielding and deflection, in short "diversion" effect whose basic sensory and behavioral mechanisms call for future exploration.     

High-throughput protein localization in Arabidopsis using Agrobacterium-mediated transient expression of GFP-ORF fusions

We describe a streamlined and systematic method for cloning green fluorescent protein (GFP)-open reading frame (ORF) fusions and assessing their subcellular localization in Arabidopsis thaliana cells. The sequencing of the Arabidopsis genome has made it feasible to undertake genome-based approaches to determine the function of each protein and define its subcellular localization. This is an essential step towards full functional analysis. The approach described here allows the economical handling of hundreds of expressed plant proteins in a timely fashion. We have integrated recombinational cloning of full-length trimmed ORF clones (available from the SSP consortium) with high-efficiency transient transformation of Arabidopsis cell cultures by a hypervirulent strain of Agrobacterium. To demonstrate its utility, we have used a selection of trimmed ORFs, representing a variety of key cellular processes and have defined the localization patterns of 155 fusion proteins. These patterns have been classified into five main categories, including cytoplasmic, nuclear, nucleolar, organellar and endomembrane compartments. Several genes annotated in GenBank as unknown have been ascribed a protein localization pattern. We also demonstrate the application of flow cytometry to estimate the transformation efficiency and cell cycle phase of the GFP-positive cells. This approach can be extended to functional studies, including the precise cellular localization and the prediction of the role of unknown proteins, the confirmation of bioinformatic predictions and proteomic experiments, such as the determination of protein interactions in vivo, and therefore has numerous applications in the post-genomic analysis of protein function.     

Ketoheterocycle-based inhibitors of cathepsin K: a novel entry into the synthesis of peptidic ketoheterocycles

Ketoheterocyclic inhibitors of cathepsin K have been disclosed. SAR of potency enhancing P2-P3 groups coupled with ketoheterocyclic warheads to provide cathepsin K inhibitors have been described. In addition, a novel route to access alpha-ketothiazoles using a key thioamide functionality has been disclosed. The mild method employed allows for the presence of diverse functional groups, such as amide and carbamate functionalities, commonly found in protease inhibitors that have peptidomimetic scaffolds. This new method should provide a quick entry into functionally diverse protease inhibitors.